Why to monitor
microscope condition?

Microscopes are sophisticated optical instruments that take extremely precise measurements on biologic samples. Therefore, it is essential not only to keep them in good condition but also to know what their condition is.

Every careful measurement in science is always given with the probable error … every observer admits that he is likely wrong, and knows about how much wrong he is likely to be.

Bertrand Russell

Key objectives of monitoring microscope condition

  1. Ensure that performance degradation is detected as soon as possible
  2. Help the core staff to diagnose the problem and react accordingly
  3. Provide evidence serving in the dialogue with microscope manufacturers and service providers
  4. Calibrate hardware
  5. Provide quality assurance and analysis data and meta-data to the users of the facility

When to monitor
microscope condition?

The monitoring of the microscope condition should be done at different moments to ensure that the equipment is performing according to a predefined specifications chart.

  • During the installation of new equipment to ensure the acceptance of the installation and establish the baseline for the future.
  • During the service life of the system:
    • after the periodic maintenance is carried out either by the core facility staff or by an external service provider.
    • when there is a doubt about the performance of the equipment.
    • when there is a change in the environment of the equipment.

Why a new tool to monitor microscope performance?

Another important text here

Current tools

There are existing tools [1, 2, 3] that are focused in producing measurements on optical standards to evaluate the performance of the equipment. However these tools are either proprietary or tightly bound to a specific GUI (ImageJ) which limits their implementation with external tools.

In this project we want to profit from the great advantages that Python offers to produce a library that integrates well with modern data analysis and management and visualization tools.

What is missing?

  • Missing feature 1
  • Missing feature 2

What is the solution?

FAIR microscope performance monitoring

How does it work?

  1. Import image data into OMERO in a well defined structure
  2. Run the analysis using predefined parameters
  3. Visualize the results in a dashboard

1. Import image data into OMERO

OMERO is a server-client platform for managing, visualizing, and analyzing microscope images and metadata.

1.1. Importing images

Acquired images are imported into OMERO following a well defined structure.

2. Run the analysis

3. Visualize the results

Functional requirements

Visualization features

microscopemetrics-dashboard should provide the possibility to implement different interfaces depending on the “access level”, in decreasing order of access privileges:

Core facility staff

Core facility QC processus

Node of National infrastructure

Core facility user

A very simple view for the user. Green-Yellow-Red In the principle it is a good thing to be transparent but difficult to report the general state of the microscope without oversimplifying. A solution might be to provide data without judgement.

Provide a configurable way to provide information. Configurable by the responsible of the core facility. Adding thresholds should be configurable too.

Handle diversity is key.

microscopemetrics-dashboard should provide, and depending on the access level, these visualization posibilities:

Display one set of key metrics over time or given period for:

One single device, including different imaging settings (objective, filter set…).

Multiple devices

Display the state of one particular device and analysis type at a point in time in a very detailed view

Comparing different machines (?).

Other features to discuss and to rank:

  • Filtering of data dans le temps. Find the timepoint where a certain value was out of specs.
  • Adding in each visualization the day 1, best, nominal, manufacturer spec measurement.
  • Adding comments in the dashboard - saved in OMERO. Standardize the format of the comments with
  • predefined key
  • date
  • human readable message
  • Save user custom layouts allowing the core staff to follow, for example: a number of limited metrics of interest to her/him, or create a custom layout of advanced metrics (more difficult to achieve). There is a training cost.
  • Alternativelly to the customizable layout, propose several models (eg. simple, detail, very detailed).
  • Quality threshold system: threshold max, min. Lists of references (industry, rt-mfm, my own threshold).
  • Color coding when values are outside of thresholds. Visual alert
  • Alerting system: e-mail… Not priority
  • Reports generation (PDF, yaml, csv).
  • Annotation of user images with QC measurements in OMERO. Low priority
  • Design a meta indicator cumulating several measurement (WGMM). To think about
  • Perfomance indicator linkable with OpenIris. Identify URI for QC data.
  • allow users to implement own measurements as reference of quality. The example of the CV measurement by each user could be used (program validj) or other metrics to be defined by users. Same kind of interface to follow laser power measurements

Deployment

The tool will be deployed by the FBI infrastructure for our use case. Docker?

Documentation

Provide developer and user documentation. Formats to define

Tools and methods

Programmatic tools

Python (Cpython) is the language of choice for developing microscope-metrics and so it will be for microscopemetrics-dashboard. A number of options ara available for developing a dashboard:

A few choices of development tools:

  • pytest for testing framework
  • black for code formatting
  • Installation using poetry

Attribution of responsibilities

FBI-core facility integration Cedric FBI-data: Guillaume Project responsible: Julio Project developer: Oumou WG-microscope-metrics: WGMM

  • Dauphin Aurelien
  • Sylvain Derossi
  • Audrey Salles
  • Erwan GRANDGIRARD

The development team will meet at least once every three months to discuss about the evolution of the project.

The WGMM will be the initial test group for every release.

Project start conditions

Financial

Not applicable at this point in time. A 12 month salary has been obtained from FBI.

Human Resources

The estimated human resources available during the length of the project are 12 months full time.

Environmental conditions

No special environmental conditions are identified.

Suspensive conditions

No special suspensive conditions are identified

Validation criteria

Provided by the code testing framework of the software. Yet to identify a test suite to test the GUI.

A test group will be put in place to test the GUI. This group must validate the development.

Development in phases

Milestones to define : 1) finalizing specifications / january 2) writing code and validation / 02-06 3) Carry out unit tests (per measure and per instrument) and integration tests (on one or more instrumental parks of a node) to ensure the proper functioning of the dashboard. 4) Validate compatibility with different OMERO databases within the perimeter of a node. parallelization of the work to design several specificities like metaparameters or custom layout

Data storage conditions

Code base is stored in GitHub. All other documentation is stored in Taiga. Code related issue tracking is managed in GitHub. Project management is done in Taiga.

Documentation

The project should be accompanied by documentation for the user and for the developer.

Licensing

The code is distributed as open source under GPL 3.0. The main reason being that it is the license used by the OME consortium.

Dissemination & communication

All tools are disseminated as open-source GPL3. Available on github.

The public interested in this tool is core facility staff. The tool will be promoted and communicated through the regular routes: meetings, work-groups, presentations,… It is foreseeable to write a paper when a stable version is released.

References

[1] Cédric Matthews and Fabrice P. Cordelieres, MetroloJ : an ImageJ plugin to help monitor microscopes’ health, in ImageJ User & Developer Conference 2010 proceedings. [2] Theer, P., Mongis, C. & Knop, M. PSFj: know your fluorescence microscope. Nat Methods 11, 981–982 (2014). doi.org/10.1038/nmeth.3102 [3] argolight.com/measure-microscopes-performances-detect-issues-with-daybook [4] https://stackoverflow.blog/2020/05/27/2020-stack-overflow-developer-survey-results/ [5] https://insights.stackoverflow.com/survey/2020